July 29th, 2014: Marvin 14.7.28.0

Improvements

Structure Representation
- Atomic masses and isotopic weights are updated to the 2013 standards and the isotope file format have changed. Documentation
- Multiple S-group cannot be expanded if it contains one or more child S-group.
- Pseudo labels are displayed centered.
MarvinSketch
- "Copy Special" dialog in the Edit menu is renamed to "Copy as".
Image I/O
- Images are exported with "fog effect" set by the user. Image export parameter "fogFactor" has been intoduced.

Import/Export
- Parity was inverted during import of 0 dimensional CML files. Forum

Editing
- Placing a graphical object (or a text box) on the canvas containing R-group definition, the position of the R group label changed as if the graphical object (or the text box) would be the part of the R-group definition.

Import/Export
- R-group members exported incorrectly SKC.
- InChi I/O did not work on MacOS with Java 1.7 or higher. Forum
- Stereo care flag was lost during compressed MOL import.
Image I/O
- Position of subscript numbers in labels changed when zooming in.
- There were patches around atom labels when EMF image was exported with transparent background.
Stereochemistry
- Retrieving parity information could change the result of the CIP stereo recognition. Forum

Editing
- R-group editing (such as connecting atoms in R-group definitions) froze MarvinSketch.
Image I/O
- Implicit H atoms and R/S stereo labels overlapped bonds on exported EMF images.

Molecule representation
- New homology groups: "heteroSubstitutedAlkyl", "haloAlkyl" and "hydroxyalkyl" were introduced. Documentation.
- Invalid input is not accepted in the R-group logic definition field.
- The terminal nucteotides are linked by bend bond in cleaned RNA/DNA sequences displayed in more than one row.
- Text formatting options were introduced for abbreviated groups and alias atoms.
- Validation was implemented for "Edit properties" dialog.

Editing
- Merging a contracted S-group while pressing shift button resulted in zero atom at the merging site.
- S-group "Bracket style=Curved" was disabled.
- In-hand contracted amino acid threw exception over an expanded amino acid.
- vmn abbreviation groups are not supported.

Clean 2D
- Clean 2D was improved in order to keep the orientation of the molecule as much as possible.
- Clean of sequences has been improved:
  - Sequences (even if they contain expanded residues) are aligned into a horizontal line and are broken into multiple lines after 20 residues. Each line is read from left to right.
  - Space is left for chemical parts connected to the third attachment of the residues, these attachments are aligned to the top of the residue. Attachments to expanded residues are also considered.
  - Chemical parts connected to the beginning and the end of the sequence are aligned to the left and to the right of the sequence.
  - Chains of sequences connected with chemical linkers are also handled: chemical linkers are aligned horizontally to the sequences to which they are connected and space is left for them between the lines of the sequences.
- Default 2-dimensional clean of bicyclic molecules has been changed. The old behaviour can be switched back by selecting 'Bicyclics' on the Template Library GUI (Insert<Template) then ticking the 'Use molecules as template at 2D cleaning' option on the 'Properties' page.

Import/Export
- Picture format 'ppm' is not supported anymore.
- New tag introduced in MRV file to store the atom properties of the abbreviation even if the Superatom S-group is expanded. Until now such properties were lost.
- Default handling of bond lengths in the import of MDL formats has changed: bond lengths are rescaled to ChemAxon standard for 2D molecules not only for V2000 format input but also for V3000.
- Character '.' which is the delimiter between atom property keys and values in CXMSMILES format is escaped, which allows the usage of '.' characters in property keys and values.
- InChi improvement: import and export of axial chirality and not specified double bond stereo are now possible.
- Atom properties set on the superatom of an abbreviation S-group can be exported to and imported from AbbrevGroup format (ChemAxon extension of smiles for abbreviated groups). Documentation

MarvinSketch Menu
- "Shapely" option was removed from View>Color menu.
- "Quality" option was removed from View>Display menu.
- "ChemAxon JChem Table format/JTF" was removed from the "Import As" dialog.
- Edit<Copy as<IUPAC Name (ASCII) option was introduced.

Calculator Plugins
- Progress indication was introduced for Marvin Services.
Applet
- "Autocheckstructure" applet parameter is available.

MolConverter
- A new option "-f" was introduced in MolConvert in order to define import format and options even if the input files are defined with a wildcard. Documentation

MarvinSketch
- If MarvinSketch was started with edit structure from MarvinView by double click on a structure NPE was thrown.
- MarvinOLEServer process was stopped when multiple MarvinSketch windows had been opened and one was closed.

MarvinGUI
- The font size in Marvin was smaller than other commercial drawing programs and text editors (such as Word).
- Font size was different on different screen resolutions.

Editing
- Abbreviated groups
  - In generic, component, monomer and mer type abbreviated groups charge was shown both on the atom and on the bracket.
  - When wedge bond(single down, single up, single up and down) was drawn between two contracted S-groups an overlay of a single and a wedge bond was created.
  - The Sgroup was not positioned correctly at contracting/expanding the group.
  - Sgroup label was not displayed in expanded form.
  - The "On atoms"/"On brackets" options were not available on the Edit Group dialog when the structure was imported.
  - Edited abbreviated group labels (except Sgroup labels) could not be saved.

Import/Export
- Import of MOL V3000 files containing aromatic wedge bonds threw MolFormatException.
- MRV importer did not read molecule properties of R-group members.
- SVG export threw exception.
- When exporting graphical objects (e.g., brackets, arrows) into pdf and image formats part of the images was cut.
- Extension ".properties" was not added atomatically to the 'File name' on the "Save style" dialog.
- Bounding rectangle was calculated incorrectly for structures displayed in Ball&Stick view and this caused incorrect image export.
- Attached data was lost upon export to png format.

Elemental Analyzer
- Molecule weight calculation could not read molecular formula with more than two dots. Forum